Your message dated Tue, 18 Jul 2023 15:04:04 +0000
with message-id <e1qlmfa-002szz...@fasolo.debian.org>
and subject line Bug#1037739: fixed in libseqlib 1.2.0+dfsg-10
has caused the Debian Bug report #1037739,
regarding libseqlib: ftbfs with GCC-13
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1037739: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037739
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:libseqlib
Version: 1.2.0+dfsg-9
Severity: normal
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/libseqlib_1.2.0+dfsg-9_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-13/porting_to.html
[...]
+#MISSING: 1.2.0+dfsg-9#
_ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb1EED1Ev@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
_ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb1EED2Ev@Base
1.2.0
_ZNSt8__detail9_Map_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS6_N6SeqLib4_BamEESaISB_ENS_10_Select1stESt8equal_toIS6_ESt4hashIS6_ENS_18_Mod_range_hashingENS_20_Default_ranged_hashENS_20_Prime_rehash_policyENS_17_Hashtable_traitsILb1ELb0ELb1EEELb1EEixERS8_@Base
1.2.0
(optional)_ZNSt8__detail9_Map_baseIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS6_EEESaIS9_ENS_10_Select1stESt8equal_toIiESt4hashIiENS_18_Mod_range_hashingENS_20_Default_ranged_hashENS_20_Prime_rehash_policyENS_17_Hashtable_traitsILb0ELb0ELb1EEELb1EEixERS2_@Base
1.2.0
_ZNSt8__detail9_StateSeqINSt7__cxx1112regex_traitsIcEEE8_M_cloneEv@Base 1.2.0
-
(optional)_ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E0_EEEvT_SK_RT0_@Base
1.2.0
-
(optional)_ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_RT0_@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
(optional)_ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E0_EEEvT_SK_RT0_@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
(optional)_ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_RT0_@Base
1.2.0
(optional)_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIP9mem_aln_tSt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops15_Iter_comp_iterIPFbRKS2_SB_EEEEvT_T0_SG_T1_T2_@Base
1.2.0
(optional)_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEElS4_NS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_T0_SL_T1_T2_@Base
1.2.0
+
_ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_SK_T0_@Base
1.2.0+dfsg-9
(optional)_ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPN6SeqLib13GenomicRegionESt6vectorIS3_SaIS3_EEEENS0_5__ops15_Iter_less_iterEEvT_SB_SB_T0_@Base
1.2.0
(optional)_ZSt13binary_searchIN9__gnu_cxx17__normal_iteratorIPKcSt6vectorIcSaIcEEEEcEbT_S8_RKT0_@Base
1.2.0
(optional)_ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEEPS4_ET0_T_SD_SC_@Base
1.2.0
@@ -559,9 +589,9 @@
(optional)_ZSt4findIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEES7_ET_SE_SE_RKT0_@Base
1.2.0
_ZSt4swapIN12aho_corasick7ahoemitIcEEENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleIS7_ESt18is_move_assignableIS7_EEE5valueEvE4typeERS7_SH_@Base
1.2.0
(optional)_ZSt4swapIN6SeqLib11PlottedReadEENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleIS6_ESt18is_move_assignableIS6_EEE5valueEvE4typeERS6_SG_@Base
1.2.0
-
(optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
(optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_@Base
1.2.0
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_@Base
1.2.0
-
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_@Base
1.2.0
_ZTINSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb0EEE@Base
1.2.0
_ZTINSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb1EEE@Base
1.2.0
_ZTINSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1ELb0EEE@Base
1.2.0
@@ -589,7 +619,7 @@
(optional)_ZTISt19_Sp_counted_deleterIP9hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTISt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTISt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
-
(optional)_ZTISt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
(optional)_ZTISt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTISt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
_ZTS10idx_delete@Base 1.2.0
_ZTS14bam_hdr_delete@Base 1.2.0
@@ -624,7 +654,7 @@
(optional)_ZTSSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTSSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
_ZTSSt19_Sp_make_shared_tag@Base 1.2.0
-
(optional)_ZTSSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
(optional)_ZTSSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTSSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTVSt15_Sp_counted_ptrIPN12aho_corasick10basic_trieIcEELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTVSt15_Sp_counted_ptrIPSt13unordered_mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4hashIS6_ESt8equal_toIS6_ESaISt4pairIKS6_iEEELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
@@ -635,7 +665,7 @@
(optional)_ZTVSt19_Sp_counted_deleterIP9hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTVSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTVSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
-
(optional)_ZTVSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
(optional)_ZTVSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
(optional)_ZTVSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base
1.2.0
_ZZNKSt7__cxx1112regex_traitsIcE16lookup_classnameIPKcEENS1_10_RegexMaskET_S6_bE12__classnames@Base
1.2.0
_ZZNKSt7__cxx1112regex_traitsIcE18lookup_collatenameIPKcEENS_12basic_stringIcSt11char_traitsIcESaIcEEET_SA_E14__collatenames@Base
1.2.0
@@ -643,10 +673,11 @@
_ZZNKSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb1EEclEcE5__nul@Base
1.2.0
_ZZNKSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1ELb0EEclEcE5__nul@Base
1.2.0
_ZZNKSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1ELb1EEclEcE5__nul@Base
1.2.0
-
(optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv@Base
1.2.0
+#MISSING: 1.2.0+dfsg-9#
(optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv@Base
1.2.0
(optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv@Base
1.2.0
(optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb1ELb0EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv@Base
1.2.0
(optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb1ELb1EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv@Base
1.2.0
_ZZNKSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EE10_M_is_wordEcE3__s@Base
1.2.0
_ZZNKSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb1EE10_M_is_wordEcE3__s@Base
1.2.0
_ZZNSt19_Sp_make_shared_tag5_S_tiEvE5__tag@Base 1.2.0
+
_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb0EEEbRNS4_13_BracketStateERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc@Base
1.2.0+dfsg-9
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: libseqlib
Source-Version: 1.2.0+dfsg-10
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
libseqlib, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1037...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated libseqlib package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 18 Jul 2023 15:56:08 +0200
Source: libseqlib
Architecture: source
Version: 1.2.0+dfsg-10
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1015520 1037739
Changes:
libseqlib (1.2.0+dfsg-10) unstable; urgency=medium
.
* d/libseqlib2.symbols.amd64: update.
Mark symbols optimized out by LTO as optional. This has the side
effect of resolving build failures with Gcc 13. (Closes: #1015520,
#1037739)
* d/control: declare compliance to standards version 4.6.2.
Checksums-Sha1:
05741dc493d4e80fd934c6a1e87180f5a4b38875 2401 libseqlib_1.2.0+dfsg-10.dsc
8e43e597e27e44363f0e2fb75cddbd61bc6e68be 15392
libseqlib_1.2.0+dfsg-10.debian.tar.xz
Checksums-Sha256:
e67b09bbe4fad1cfe589eb8fc13dd78ec70d0f4f79c48c63d878cd88075f7e62 2401
libseqlib_1.2.0+dfsg-10.dsc
8cfea0609affd3f509ce28729d965da819ef85a005ac4426225265fb086b9c31 15392
libseqlib_1.2.0+dfsg-10.debian.tar.xz
Files:
49be9964de583eaf62ffef6398543e8f 2401 science optional
libseqlib_1.2.0+dfsg-10.dsc
d67b2b6e1009f099ab5f01525703b11e 15392 science optional
libseqlib_1.2.0+dfsg-10.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmS2on8UHGVtb2xsaWVy
QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpNLA/+OZnTBr97B6tCRBtbHYOosUfb28GJ
9e5gStx3g/u96poV08+bqHBeFc2NdKJcWlQyFJ17bujlfVnQj2ft/i2yKWksqLsS
stkZwGZLfTFdwXV/egb63cDQkQrakBCNHDF4gJWe+eASrSJgengvtC+bRBb7kz8I
TqpjZ0XVa4r+kaMB8KwbV1DRkQ4NKsWtunMAbZ3FPrcIyWJo74b/p14rgyiPUjO6
/OqJogASW6VsFademHyJARKzEVRYzO8QAcmBcdtpV7s821CDfbwId/DX3SUXfVev
Ge0kn3hmxfZtna70rJgJNU0jW4ZWTWsnaq88n6ZLgCGdlpM7NeWvQ+Gs9K57SPnG
WbCbNp+e1/jHfyRbMropuZNeRCq2s9ca+X4St/2GzVeRfOW0pn0DBfEbdgmjyxHk
iIWCv37gSQ0xleuMjKSh5gb8QghsNh0CFQiXemaVilH78GD52TFJi/99wKmrMATz
lsYuYG4k0jTh3oTa/qZNImP6gaoKS9WxAersPkiR4WtDRW6XMadjivpvhVnQQ6bx
qNi056e7oH7kfGxP1SkIwKzfiJg69OmZ0wV68QVZIYSFbmbUk9QuDlugyKmp2pFw
27ClMCYPQDzBDab+iQ5H0HlLhy3KhDI7pGxuUWy2W8wZrqpZLQKaPrQNbhtaHqJD
EYjXy1VBRLd/y9s=
=p3e/
-----END PGP SIGNATURE-----
--- End Message ---